py4cytoscape.networks.create_igraph_from_network

create_igraph_from_network(network=None, base_url='http://127.0.0.1:1234/v1')[source]

Create an igraph network from a Cytoscape network.

Notes

Takes a Cytoscape network and translates it nodes and edges into vertices and edges in igraph. Associated table columns will also be passed to igraph as vertex and edge attributes. All networks are implicitly modeled as directed in Cytoscape. Round-trip conversion of an undirected network in igraph via createNetworkFromIgraph to Cytoscape and back to igraph will result in a directed network.

Parameters

  • network (SUID or str or None) – Name or SUID of a network or view. Default is the “current” network active in Cytoscape.

  • base_url (str) – Ignore unless you need to specify a custom domain, port or version to connect to the CyREST API. Default is http://127.0.0.1:1234 and the latest version of the CyREST API supported by this version of py4cytoscape.

Returns

The new igraph object

Return type

igraph

Raises

  • ValueError – if server response has no JSON

  • CyError – if network name or SUID doesn’t exist

  • requests.exceptions.RequestException – if can’t connect to Cytoscape or Cytoscape returns an error

Examples

>>> create_igraph_from_network()
IGRAPH DN-- 330 359 --
+ attr: AverageShortestPathLength (v), BetweennessCentrality (v), COMMON (v),
  ClosenessCentrality (v), ClusteringCoefficient (v), Degree (v), Eccentricity
  (v), IsSingleNode (v), NeighborhoodConnectivity (v), NumberOfDirectedEdges
  (v), NumberOfUndirectedEdges (v), PartnerOfMultiEdgedNodePairs (v),
  Radiality (v), SelfLoops (v), Stress (v), TopologicalCoefficient (v),
  degree.layout (v), gal1RGexp (v), gal1RGsig (v), gal4RGexp (v), gal4RGsig
  (v), gal80Rexp (v), gal80Rsig (v), isExcludedFromPaths (v), name (v),
  selected (v), shared name (v), EdgeBetweenness (e), interaction (e), name
  (e), selected (e), shared interaction (e), shared name (e), source (e),
  target (e)
+ edges (vertex names):
YML064C->YLR284C, YML064C->YHR198C, YKL074C->YGL035C, YDL081C->YLR340W,
...

See also

create_network_from_data_frames(), create_network_from_igraph()